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@ARTICLE{BM08,
  author = {J.~Butler and I.~MacCallum and M.~Kleber and I.A.~Shlyakhter and
	M.K~Belmonte and E.S~Lander and C.~Nusbaum and D.B~Jaffe},
  title = {ALLPATHS: de novo assembly of whole-genome shotgun microreads},
  journal = {Genome Research},
  year = {2008},
  volume = {18},
  pages = {810-20},
  number = {5},
  owner = {sergey},
  timestamp = {2011.05.22}
}

@ARTICLE{CBP09,
  author = {M.J.~Chaisson and D.~Brinza and P.A.~Pevzner},
  title = {De novo fragment assembly with short mate-paired reads: Does the
	read length matter?},
  journal = {Genome Research},
  year = {2009},
  volume = {19},
  pages = {336-346},
  owner = {sergey},
  timestamp = {2011.05.21}
}

@ARTICLE{CP08,
  author = {M.J.~Chaisson and P.A.~Pevzner},
  title = {Short read fragment assembly of bacterial genomes},
  journal = {Genome Research},
  year = {2008},
  volume = {18},
  pages = {324-330},
  owner = {sergey},
  timestamp = {2011.05.21}
}

@ARTICLE{CPT04,
  author = {M. Chaisson and P. Pevzner and H. Tang},
  title = {Fragment assembly with short reads},
  journal = {Bioinformatics},
  year = {2004},
  volume = {20},
  pages = {2067-2074},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{CP10,
  author = {P.~Compeau and P.~Pevzner},
  title = {Genome Reconstruction: A Puzzle with a Billion Pieces},
  year = {2010},
  owner = {sergey},
  timestamp = {2011.05.21}
}

@ARTICLE{HG01,
  author = {International Human Genome Sequencing Consortium},
  title = {Initial sequencing and analysis of the human genome},
  journal = {Nature},
  year = {2001},
  volume = {409},
  pages = {860–921},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{DMS10,
  author = {A. Dayarian and T.P. Michael and A.M. Sengupta},
  title = {SOPRA: Scaffolding algorithm for paired reads via statistical optimization},
  journal = {BMC Bioinformatics},
  year = {2010},
  volume = {11},
  owner = {sergey},
  timestamp = {2011.05.28}
}

@BOOK{IBA,
  title = {An Introduction to Bioinformatics Algorithms},
  publisher = {The MIT Press},
  year = {2004},
  author = {N. Jones and P.Pevzner},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{KSS10,
  author = {D.R.~Kelley and M.C.~Schatz and S.L.~Salzberg},
  title = {Quake: quality-aware detection and correction of sequencing errors
	2010 11(11):R116.},
  journal = {Genome Biology},
  year = {2010},
  volume = {11},
  owner = {sergey},
  timestamp = {2011.05.22}
}

@ARTICLE{LZR10,
  author = {Ruiqiang Li and Hongmei Zhu and Jue Ruan, et al.},
  title = {De novo assembly of human genomes with massively parallel short read
	sequencing},
  journal = {Genome Research},
  year = {2010},
  volume = {20},
  pages = {265-272},
  owner = {sergey},
  timestamp = {2011.05.28}
}

@ARTICLE{AP2,
  author = {I. MacCallum and D. Przybylski and S. Gnerre1 and J. Burton},
  title = {ALLPATHS 2: small genomes assembled accurately and with high continuity
	from short paired reads},
  journal = {Genome Biology},
  year = {2009},
  volume = {10},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{M05,
  author = {E. Myers},
  title = {The fragment assembly string graph},
  journal = {Bioinformatics},
  year = {2005},
  volume = {21},
  pages = {1179–1185},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{PS10,
  author = {K. Paszkiewicz and D.J. Studholme},
  title = {De novo assembly of short sequence reads},
  journal = {Briefings in bioinformatics},
  year = {2010},
  volume = {11},
  pages = {457-472},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{PT01,
  author = {P.A.~Pevzner and H.~Tang},
  title = {Fragment assembly with double-barreled data},
  journal = {Bioinformatics},
  year = {2001},
  volume = {17},
  pages = {225-33},
  owner = {sergey},
  timestamp = {2011.05.21}
}

@INPROCEEDINGS{PTW01,
  author = {P.A.~Pevzner and H.~Tang and M.S.~Waterman},
  title = {An Eulerian path approach to DNA fragment assembly},
  booktitle = {Proceedings of the National Academy of Sciences of the United States
	of America},
  year = {2001},
  volume = {98},
  number = {17},
  pages = {9748–9753},
  owner = {sergey},
  timestamp = {2011.05.21}
}

@ARTICLE{SDS10,
  author = {M.C.~Schatz and A.L.~Delcher and S.L.~Salzberg},
  title = {Assembly of large genomes using second-generation sequencing},
  journal = {Genome research},
  year = {2010},
  volume = {20},
  pages = {1165-73},
  number = {9},
  owner = {sergey},
  timestamp = {2011.05.21}
}

@ARTICLE{SJ08,
  author = {J. Shendure and H. Ji},
  title = {Next-generation DNA sequencing},
  journal = {Nat Biotechnol},
  year = {2008},
  volume = {26},
  pages = {1135-1145},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{SWJ09,
  author = {J.T. Simpson and K. Wong and S.D. Jackman},
  title = {ABySS: A parallel assembler for short read sequence data},
  journal = {Genome research},
  year = {2009},
  owner = {sergey},
  timestamp = {2011.05.28}
}

@ARTICLE{ZMMB09,
  author = {D. Zerbino and G. McEwen and E. Margulies and E. Birney},
  title = {Pebble and rock band: heuristic resolution of repeats and scaffolding
	in the velvet short-read de novo assembler},
  journal = {NCBI},
  year = {2009},
  volume = {4},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@ARTICLE{ZB08,
  author = {Daniel R.~Zerbino and Ewan Birney},
  title = {Velvet: Algorithms for de novo short read assembly using de Bruijn
	graphs},
  journal = {Genome Research},
  year = {2008},
  volume = {18},
  pages = {821-829},
  owner = {sergey},
  timestamp = {2011.05.21}
}

@MASTERSTHESIS{DV10,
  author = {М.Э. Дворкин},
  title = {Алгоритм секвенирования ДНК на основе парных цепей},
  school = {СПбГУ ИТМО},
  year = {2010},
  owner = {sergey},
  timestamp = {2011.06.06}
}

@misc{QURL,
  title = {Quake, http://www.cbcb.umd.edu/software/quake},
  url = {http://www.cbcb.umd.edu/software/quake},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@misc{SDN,
  title = {SOAP de novo, http://soap.genomics.org.cn/soapdenovo.html},
  url = {http://soap.genomics.org.cn/soapdenovo.html},
  owner = {sergey},
  timestamp = {2011.06.07}
}

@misc{VVT,
  title = {Velvet, http://www.ebi.ac.uk/~zerbino/velvet/},
  url = {http://www.ebi.ac.uk/~zerbino/velvet/},
  owner = {sergey},
  timestamp = {2011.06.07}
}


@book{ gusfield,
    author =       "Гасфилд Дэн",
    title =        "Строки, деревья и последовательности в алгоритмах: Информатика и вычислительная биология.",
    address =      "СПб.",
    publisher =    "Невский диалект; БХВ-Петербург",
    year =         "2003",
}

@misc{ superstring,
	title = "The Shortest Superstring Problem, http://www.cs.ust.hk/~golin/COMP670J",
	url = "http://www.cs.ust.hk/~golin/COMP670J/Lecture4.ps"
}

@misc{ ABYSS,
	title =	"ABySS, http://www.bcgsc.ca/platform/bioinfo/software/abyss",
	url =	"http://www.bcgsc.ca/platform/bioinfo/software/abyss"
}


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